I went through the same thing!
My first paid project was doing the aprons for a diner down the street. So, for 15 aprons I offered no set up fee--that's what was super expensive for the business owner, 90 dollars to get her logo digitized, MORE if she wanted text added to the logo. The price per embroidery wasn't too different. Since it was my first big job I charged less than I do now, I only charged a measly $6 an apron, since I didn't know how reliably I could line up the design on the apron pockets. But, that was $90 for and hour and a half of work and only about $5 dollars of overhead worth of backing, thread, and electricity. Half an hour to digitize and test run a sample on cheap fabric, then I traded the sample for a box of aprons and ran the aprons while watching TV. So, yeah, I probably undersold the product, but it was worth it to guarantee the deal, since now if people ask about my work I can tell them to go eat at the diner and see for themselves!
After that I've been charging based on the number of colors, the size, and whether it's a specialty gift embroidery or a short run. For a one or two item embroidery for a special gift, people will pay a lot more per embroidery than for a "short run" run project. So charging differently for short run and "specialty gifts" is probably a good idea.
Where you live affects price. If I was still in Seattle I'd charge $30 per monogram or text embroidery, but here I have to charge $15, then charge more for designs and such.

I think the biggest thing is to charge a price that makes it "worth it" for you. If you feel that pinning hoopless designs and changing colors is a big pain in the butt, then charge an amount that makes you feel its worth your time! If I charge $30 here I don't get many customers, but I do still get customers, my machine pays for its own supplies, and I feel excited and happy to do the job. The $15 dollar embroideries are kind of painful, but I like getting practice so I do them anyway.